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| 1st(1st leg) | Gabala FK | - | Dinamo Moskva | 0:2 (0:1) | ||
| 2nd (2nd leg) | Dinamo Moskva | - | Gabala FK | 5:0 (1:0) | ||
| 1st(1st leg): 21/09/2016 16:00 | 2nd (2nd leg): 19/10/2016 16:00 | Winner: Dinamo Moskva | ||||
| 1st(1st leg) | RB Salzburg | - | Vardar Skopje | 5:0 (3:0) | ||
| 2nd (2nd leg) | Vardar Skopje | - | RB Salzburg | 0:3 (0:0) | ||
| 1st(1st leg): 27/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 18:00 | Winner: RB Salzburg | ||||
| 1st(1st leg) | RSC Anderlecht | - | FC Midtjylland | 0:0 (0:0) | ||
| 2nd (2nd leg) | FC Midtjylland | - | RSC Anderlecht | 3:1 (1:0) | ||
| 1st(1st leg): 27/09/2016 18:00 | 2nd (2nd leg): 19/10/2016 18:00 | Winner: FC Midtjylland | ||||
| 1st(1st leg) | AC Sparta Praha | - | OFK Titograd | 4:0 (3:0) | ||
| 2nd (2nd leg) | OFK Titograd | - | AC Sparta Praha | 0:5 (0:3) | ||
| 1st(1st leg): 28/09/2016 13:00 | 2nd (2nd leg): 19/10/2016 12:30 | Winner: AC Sparta Praha | ||||
| 1st(1st leg) | APOEL Nikosia | - | AS Roma | 0:3 (0:2) | ||
| 2nd (2nd leg) | AS Roma | - | APOEL Nikosia | 6:1 (2:0) | ||
| 1st(1st leg): 28/09/2016 14:00 | 2nd (2nd leg): 19/10/2016 14:30 | Winner: AS Roma | ||||
| 1st(1st leg) | Altınordu FK | - | Levski Sofia | 5:0 (2:0) | ||
| 2nd (2nd leg) | Levski Sofia | - | Altınordu FK | 1:1 (1:0) | ||
| 1st(1st leg): 28/09/2016 16:00 | 2nd (2nd leg): 19/10/2016 15:00 | Winner: Altınordu FK | ||||
| 1st(1st leg) | FC Nitra | - | Málaga CF | 2:3 (1:0) | ||
| 2nd (2nd leg) | Málaga CF | - | FC Nitra | 5:0 (2:0) | ||
| 1st(1st leg): 28/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 17:00 | Winner: Málaga CF | ||||
| 1st(1st leg) | Puskás FC | - | PAOK Saloniki | 1:1 (0:0) | ||
| 2nd (2nd leg) | PAOK Saloniki | - | Puskás FC | 0:0 (0:0) | ||
| 1st(1st leg): 28/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 16:00 | Winner: PAOK Saloniki | ||||
| 1st(1st leg) | NK Domžale | - | FK Čukarički | 1:1 (0:0) | ||
| 2nd (2nd leg) | FK Čukarički | - | NK Domžale | 4:1 (1:0) | ||
| 1st(1st leg): 28/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 17:00 | Winner: FK Čukarički | ||||
| 1st(1st leg) | Breiðablik | - | AFC Ajax | 0:3 (0:2) | ||
| 2nd (2nd leg) | AFC Ajax | - | Breiðablik | 4:0 (3:0) | ||
| 1st(1st leg): 28/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 18:00 | Winner: AFC Ajax | ||||
| 1st(1st leg) | HJK Helsinki | - | Cork City | 0:0 (0:0) | ||
| 2nd (2nd leg) | Cork City | - | HJK Helsinki | 1:0 (0:0) | ||
| 1st(1st leg): 28/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 19:00 | Winner: Cork City | ||||
| 1st(1st leg) | Rosenborg BK | - | AIK Solna | 0:0 (0:0) | ||
| 2nd (2nd leg) | AIK Solna | - | Rosenborg BK | 1:3 (1:2) | ||
| 1st(1st leg): 28/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 17:00 | Winner: Rosenborg BK | ||||
| 1st(1st leg) | FC Viitorul Constanța | - | FC Sheriff | 4:1 (2:1) | ||
| 2nd (2nd leg) | FC Sheriff | - | FC Viitorul Constanța | 0:1 (0:1) | ||
| 1st(1st leg): 28/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 16:00 | Winner: FC Viitorul Constanța | ||||
| 1st(1st leg) | Zrinjski Mostar | - | FC Zürich | 0:3 (0:2) | ||
| 2nd (2nd leg) | FC Zürich | - | Zrinjski Mostar | 6:0 (2:0) | ||
| 1st(1st leg): 28/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 16:00 | Winner: FC Zürich | ||||
| 1st(1st leg) | Dinamo Tbilisi | - | FK Kairat | 0:3 (0:0) | ||
| 2nd (2nd leg) | FK Kairat | - | Dinamo Tbilisi | 5:1 (0:1) | ||
| 1st(1st leg): 29/09/2016 17:00 | 2nd (2nd leg): 19/10/2016 14:00 | Winner: FK Kairat | ||||
| 1st(1st leg) | Maccabi Haifa | - | Shakhter Soligorsk | 5:0 (1:0) | ||
| 2nd (2nd leg) | Shakhter Soligorsk | - | Maccabi Haifa | 2:3 (0:3) | ||
| 1st(1st leg): 05/10/2016 16:00 | 2nd (2nd leg): 19/10/2016 17:00 | Winner: Maccabi Haifa | ||||
